Difference between revisions of "GBrowse"

From GMOD
Jump to: navigation, search
Line 2: Line 2:
 
__NOTITLE__
 
__NOTITLE__
  
{{ComponentBox|{{GBrowseResourcesBoxItem}}|<!--{{ComponentBoxEventsHeader}}|{{GMODAmericas2011BoxItem|2011 GMOD Spring Training|GMOD Spring Training|March 8-12}}-->|||| }}
+
{{ComponentBox|{{GBrowseResourcesBoxItem}}|{{ComponentBoxEventsHeader}}|{{SchoolBoxItem|GBrowse}}|||| }}
  
 
The Generic Genome Browser (GBrowse) is a genome [[Visualization|viewer]] and is [[GMOD]]'s most popular [[GMOD Components|component]]. For a demo of its features, see [http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase], [http://flybase.org/cgi-bin/gbrowse/dmel FlyBase], and  [[GMOD_Users|others]].
 
The Generic Genome Browser (GBrowse) is a genome [[Visualization|viewer]] and is [[GMOD]]'s most popular [[GMOD Components|component]]. For a demo of its features, see [http://www.wormbase.org/tools/genome/gbrowse/c_elegans/ WormBase], [http://flybase.org/cgi-bin/gbrowse/dmel FlyBase], and  [[GMOD_Users|others]].

Revision as of 07:05, 28 June 2012

http://gmod.org/wiki/GBrowse#Logo}}

__NOTITLE__

The Generic Genome Browser (GBrowse) is a genome viewer and is GMOD's most popular component. For a demo of its features, see WormBase, FlyBase, and others.

Description

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Some of its features include:

GBrowse Versions

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

GBrowse 1.X (currently 1.70) is the older series that has been in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.

GBrowse 2.0 is a rewrite of the original GBrowse to add dynamic updating via AJAX and a smoother user experience. In addition, it provides administrators with the ability to attach a different genome database to each GBrowse track, making it much easier to manage and update tracks. It also provides a distributed backend system of "slave" renderers, allowing each track to be rendered in parallel on a different machine and significantly increasing performance. GBrowse 2.0 is considered stable,but does not have full internationalization support. In addition, there may be issues with older browsers that do not support newer JavaScript features.

Installation

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

For installing GBrowse2, please see this HOWTO.

GBrowse is Perl-based. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. See the step-by-step instructions below for detailed instructions:

Documentation

On-line documentation

GBrowse 1.x GBrowse 2.0
Usage OpenHelix Tutorial
Install Wiki Wiki
Configure Wiki / Tutorial Wiki / Tutorial


POD documentation

There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod:

Since these are in Perl POD format these files may contain formatting code when viewed in a Web browser.

Downloads

Source Code Download (tar.gz file)

Download the source from the SourceForge download page.

Net-based Installer Script

The net installer script, called gbrowse_netinstall.pl at the GBrowse GitHub repository will automatically download and install GBrowse 1.70 (NOT GBrowse2 and its Perl libraries for you. See Installation for details on using this script.

GitHub

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use GitHub. The recommended branch to use is master, which is usually stable:

 git clone https://github.com/GMOD/GBrowse.git

or, if you have commit priveleges on the GBrowse repository, you can use:

 git clone git@github.com:GMOD/GBrowse.git

which downloads significantly faster.

Once you have successfully cloned the GBrowse repository, fetch recent changes by executing git pull inside the GBrowse directory.

You can also browse the GBrowse GitHub repository.

1.x Development Version

The link above will get you to the GBrowse2 development version. To get to the GBrowse 1.x development branch, use the stable branch:

 git clone https://github.com/GMOD/GBrowse.git
 cd GBrowse
 git checkout -t -b stable origin/stable

Further reading

About Databases

GBrowse has a flexible adaptor (yes, it is spelled that way and is not "adapter") system for running off various types of databases/sources. A common question is "which adaptor should I be using?" This attempts to answer that question.

Adaptor Other required software Roughly how many users Pros Cons
Bio::DB::SeqFeature::Store (use bp_seqfeature_load.pl) MySQL, PostgreSQL, SQLite, BerkeleyDB Many and growing fast. Roughly 4X faster than Bio::DB::GFF for the same data; designed to work with GFF3 Developed for use with GFF3; about 2X slower than Bio::DB::GFF to load a database
Bio::DB::GFF (use bp_load_gff.pl, bp_bulk_load_gff.pl, bp_fast_load_gff.pl) A relational database server: MySQL, PostgreSQL, Oracle, or BerkeleyDB Lots! (Especially MySQL) Quite fast; large user base; Have to use this if your data is in the (now deprecated) GFF2 format. Does not work well with GFF3 formatted data
Bio::DB::Sam (available from CPAN) SAMtools Growing (particularly with GBrowse2) Very fast access to NextGen sequencing data Difficult to use with GBrowse 1.70
Bio::DB::BigWig and Bio::DB::BigWigSet (available from CPAN) UCSC Formats Growing (particularly with GBrowse2) Very fast access to data in bigWig format Difficult to use with GBrowse 1.70
Bio::DB::BigBed (available from CPAN) UCSC Formats Growing (particularly with GBrowse2) Very fast access to data in bigBed format Difficult to use with GBrowse 1.70
Bio::DB::Das::Chado (available from CPAN) PostgreSQL and a Chado schema Relatively few due to the specialized nature of Chado Allows 'live' viewing of the features in a Chado database Slow compared to Bio::DB::GFF
Bio::DB::Das::BioSQL (available from CPAN) MySQL and a BioSQL schema Relatively few due to the small number of BioSQL users Allows 'live' viewing of the features in a BioSQL database Slow compared to Bio::DB::GFF
Memory (ie, flat file database using either Bio::DB::GFF or SeqFeature::Store) None For real servers, none Easy for rapid development and testing Very slow for more than a few thousand features
LuceGene Lucene (searches indexed flat files) Relatively few

Email Threads

There have been some useful email threads on adaptor choices and tradeoffs.

Contacts

Please report bugs to the SourceForge Bug Tracker (select 'Category: Gbrowse').

Mailing List Link Description Archive(s)
GBrowse & GBrowse_syn gmod-gbrowse GBrowse and GBrowse_syn users and developers. Gmane, Nabble (2010/05+), Sourceforge
gmod-gbrowse-cmts Code updates. Sourceforge

The GBrowse logo was created by Alex Read, a participant in the Spring 2010 Logo Program, while a design student at Linn-Benton Community College.

References

See Also

Installation and Setup

GBrowse 2.0 Install HOWTOAdvancedInstall PathsCygwinGentooMac OS XUbuntuWindowsMigrating from GBrowse 1.X to 2.XGBrowse 1.X Install HOWTO

Configuration

GBrowse 2.0 HOWTOGBrowse Configuration HOWTOAuthenticationBalloonsDASFeature Frequency HistogramsGlyphsI18nImagesURL schemaSubtracksGBrowse AdaptorsGBrowse Backends

Development

GBrowse Persistent Variables

Other

Balloon TipsGBrowse imgRubber Band SelectionGlyphs and Glyph OptionsGbrowse BenchmarkingGBrowse User UploadsGBrowse FAQ

See also Category:GBrowse


Retrieved from "http://gmod.org/mediawiki/index.php?title=GBrowse&oldid=20716"